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Guide

Human Genome Resources Guide - overview of available human genome data resources. Includes bulletins and progress reports concerning the Human Genome Project and provides centralized access to previously disparate data. http://www.ncbi.nlm.nih.gov/genome/guide/human

Genes

Entrez Gene - gene-based resource supplying connections for map, sequence, expression, structure, functional and homology data. This data base is considered to be the successor to LocusLink. http://www.ncbi.nih.gov/gene

HomoloGene - a gene homology tool that compares nucleotide sequences between pairs of organisms in order to identify putative orthologs. Curated orthologs are incorporated from a variety of sources via LocusLink. Organisms represented are listed on the HomoloGene home page. http://www.ncbi.nlm.nih.gov/HomoloGene/

OMIMTM- Online Mendelian Inheritance in Man - continuously updated catalog of human genes and genetic disorders, with links to associated literature references, sequence records, maps, and related databases. http://www.ncbi.nlm.nih.gov/omim

RefSeq - Reference Sequences - (see "Sequences")

UniGene - ESTs and full-length mRNA sequences organized into clusters that each represent a unique known or putative gene. Annotated with mapping and expression information and cross-references to other resources. http://www.ncbi.nlm.nih.gov/unigene

Sequences

dbEST - Database of Expressed Sequence Tags - database of expressed sequence tags; short, single pass read cDNA (mRNA) sequences. Also includes cDNA sequences from differential display experiments and RACE experiments. http://www.ncbi.nlm.nih.gov/dbEST/

dbGSS - Database of Genome Survey Sequences - database of genome survey sequences; short, single pass read genomic sequences, exon trapped sequences, cosmid/BAC/YAC ends, others. http://www.ncbi.nlm.nih.gov/dbGSS/

Entrez - provides integrated access to nucleotide and protein sequence data from over 160,000 organisms, along with 3D protein structures, genetic mapping information, PubMed®, MEDLINE®, taxonomy and more. Sequence data is combined from various sources, including GenBank®, EMBL, DDBJ, RefSeq, PIR-International, PRF, Swiss-Prot, and PDB. Two unique features of Entrez are pre-computed similarity searches for each database record, identifying the related records ("neighbors") within that database, and links from a record in one database to associated records in the other Entrez databases, providing integrated access across the various databases. http://www.ncbi.nlm.nih.gov/Entrez/

HomoloGene - (see "Genes")

Human Genome Sequencing - sequencing progress of the Human Genome Project; links to chromosome views in the Map Viewer, including sequence maps assembled from contigs that were constructed from international sequencing center data; list of genome sequencing centers. http://www.ncbi.nlm.nih.gov/genome/seq/

RefSeq - Reference Sequences - curated, non-redundant set including genomic DNA contigs, mRNAs and proteins for known genes, mRNAs and proteins for gene models, and entire chromosomes. http://www.ncbi.nlm.nih.gov/RefSeq/

Trace Archive - a repository of the raw sequence traces generated by large sequencing projects that allows retrieval of both the sequence file and the underlying data which generated the file. In the case of projects that rely on a Whole Genome Shotgun (WGS) strategy, the Trace Archive will be the sole source of raw sequence data. http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?

Genome Maps

Entrez Genomes - whole genomes of over 1100 organisms as well as representation of both completely sequenced organisms and those for which sequencing is in progress. All three main domains of life - bacteria, archaea, and eukaryota - are represented, as well as many viruses, viroids, plasmids, and organelles. Also provides graphical overviews of complete genomes/chromosomes, and the ability to explore regions of interest in progressively greater detail. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Genome

Human-Mouse Homology Maps - a table comparing genes in homologous segments of DNA from human and mouse, sorted by position in each genome. Computed by integrating orthologs identified at the Jackson Laboratory with putative orthologs identified by sequence homology. http://www.ncbi.nlm.nih.gov/Homology/

Map Viewer - a software component of Entrez Genomes that allows one to view and search an organism's complete genome, display chromosome maps, and zoom into progressively greater levels of detail, down to the sequence data for a region of interest. If multiple maps are available for a chromosome, it displays them aligned to each other based on shared marker and gene names, and, for the sequence maps, based on a common sequence coordinate system. http://www.ncbi.nlm.nih.gov/mapview/

OMIM Gene Map - cytogenetic map locations of disease genes and other expressed genes described in OMIM. Can be searched by gene symbol, chromosomal location, or disorder keyword. Accessible from the OMIM page (see "Genes").

OMIM Morbid Map - (see " Disorders")

Mapped Markers

dbSTS - Database of Sequence Tagged Sites - database of sequence tagged sites; short sequences that are operationally unique in the genome, used to generate mapping reagents. http://www.ncbi.nlm.nih.gov/dbSTS/

e-PCR - Electronic PCR - compare a query sequence to mapped sequence-tagged sites (STSs) to find a possible map location for the query sequence. E-PCR finds STSs in DNA sequences by searching for subsequences that closely match the PCR primers present in mapped markers. http://www.ncbi.nlm.nih.gov/genome/sts/epcr.cgi

Human Genome Sequencing - (see "Sequences)

UniSTS - a unified, non-redundant view of sequence tagged sites (STSs) integrating marker and mapping data from a variety of public resources. If two or more markers have different names but the same primer pair, a single STS record is presented for the primer pair and all the marker names are shown. Each UniSTS record displays the primer sequences, product size, mapping information, and cross references to LocusLink, dbSNP, RHdb, GDB, MGD, and the Map Viewer. http://www.ncbi.nlm.nih.gov/unists

Genetic Variations

dbSNP - Database of Single Nucleotide Polymorphisms - NCBI database of single nucleotide polymorphisms, small-scale insertions and deletions, polymorphic repetitive elements, and microsatellite variation. dbSNP includes polymorphism data that is experimentally derived, computationally derived, as well as hybrid data that is determined by the alignment of an experimentally derived molecule to genomic sequence data. http://www.ncbi.nlm.nih.gov/SNP/

OMIM™ - Online Mendelian Inheritance in Man - allelic variants in ~900 (9%) of OMIM records. To view a list of those OMIM records, search for '0001'  in the Allelic Variant field. Or, combine a disease name with '0001'. E.g., Gaucher & 0001 [variant_text] (see "Genes").

Gene Expression

GEO - Gene Expression Omnibus - a gene expression data repository and online resource for the retrieval of gene expression data from any organism or artificial source. http://www.ncbi.nlm.nih.gov/geo/

SAGEmap - online tool to compare computed gene expression profiles between SAGE libraries generated by the Cancer Genome Anatomy Project and submitted by others through the Gene Expression Omnibus (GEO, described above). SAGEmap also includes a comprehensive analysis of SAGE tags in human GenBank records, in which a UniGene identifier is assigned to each human sequence that contains a SAGE tag. http://www.ncbi.nlm.nih.gov/SAGE/

Disorders

Genes and Disease - introduction to the relationship between genetic factors and human disease. Summary information for over 100 genetic diseases with links to related databases and organizations. http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=gnd

OMIM - Online Mendelian Inheritance in Man - (see "Genes")

OMIM Morbid Map - presents the cytogenetic map location of disease genes described in OMIM. Accessible from OMIM page (see "Genes").

SAGE Libraries Analysis - differential expression of SAGE tags in cancer libraries (see "Gene Expression").

SKY/CGH - Spectral Karyotyping and Comparative Genomic Hybridization Database - repository of publicly submitted data from SKY and CGH, which are complementary fluorescent molecular cytogenetic techniques. SKY facilitates identification of chromosomal aberrations; CGH can be used to generate a map of DNA copy number changes in tumor genomes. http://www.ncbi.nlm.nih.gov/sky/

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